Spearman correlation across replicates is low using a barcode threshold per oligo of 5! Spearman correlation of DNA is 0.29, RNA is 0.58 and DNA/RNA ratio is 0.52. Minimum allowed values are 0.85, 0.95, and 0.75.
QC Measures
Oligo Coorelatioin
Oligo correlation plots of DNA, RNA and DNA/RNA ratios across replicates. First tab shows plots using (in average) 1567 oligos with a minimum number of 5 barcodes. Second tab shows all 2016 oligos that have assigned barcodes.
| Condition | A | B | #Oligos A | #Oligos B | #Oligos Joined | DNA spearman | RNA spearman | Ratio spearman | DNA log2 pearson | RNA log2 pearson | Ratio log2 pearson |
|---|---|---|---|---|---|---|---|---|---|---|---|
| HepG2 | 1 | 2 | 1662 | 1684 | 1564 | 0.33 | 0.60 | 0.53 | 0.32 | 0.70 | 0.62 |
| HepG2 | 1 | 3 | 1662 | 1700 | 1556 | 0.29 | 0.61 | 0.55 | 0.28 | 0.71 | 0.63 |
| HepG2 | 2 | 3 | 1684 | 1700 | 1582 | 0.31 | 0.58 | 0.52 | 0.31 | 0.68 | 0.62 |
| Condition | A | B | #Oligos A | #Oligos B | #Oligos Joined | DNA spearman | RNA spearman | Ratio spearman | DNA log2 pearson | RNA log2 pearson | Ratio log2 pearson |
|---|---|---|---|---|---|---|---|---|---|---|---|
| HepG2 | 1 | 2 | 2031 | 2028 | 2016 | 0.28 | 0.53 | 0.45 | 0.27 | 0.61 | 0.51 |
| HepG2 | 1 | 3 | 2031 | 2030 | 2018 | 0.27 | 0.53 | 0.46 | 0.26 | 0.59 | 0.51 |
| HepG2 | 2 | 3 | 2028 | 2030 | 2016 | 0.28 | 0.51 | 0.43 | 0.28 | 0.58 | 0.50 |
Experiment statistic
The total number of oligos in this experiment is 2050 (defined by the assignment) with 58369 associated barcodes.
In average across replicates we see 2030 from 25281 average barcodes in the count data and around 71255 barcodes where not in the assignment.
| condition | replicate | oligos dna/rna | matched barcodes | unknown barcodes dna/rna | % matched barcodes | total dna counts | total rna counts | avg dna counts per bc | avg rna counts per bc | avg dna/rna barcodes per oligo |
|---|---|---|---|---|---|---|---|---|---|---|
| HepG2 | 1 | 2031 | 25038 | 71955 | 25.81 | 212037 | 566550 | 2.19 | 5.84 | 12.33 |
| HepG2 | 2 | 2028 | 25420 | 71141 | 26.33 | 201559 | 564222 | 2.09 | 5.84 | 12.53 |
| HepG2 | 3 | 2030 | 25384 | 70668 | 26.43 | 197109 | 601951 | 2.05 | 6.27 | 12.50 |
| Experiment | Barcodes | Counts | Average counts | Assigned barcodes | Assigned counts | Average assigned counts | Fraction assigned barcodes | Fraction assigned counts |
|---|---|---|---|---|---|---|---|---|
| HepG2_1_DNA | 149172 | 294136 | 1.97 | 32993 | 75057 | 2.27 | 0.22 | 0.26 |
| HepG2_2_DNA | 153364 | 289183 | 1.89 | 34261 | 74150 | 2.16 | 0.22 | 0.26 |
| HepG2_3_DNA | 152734 | 285380 | 1.87 | 34281 | 73508 | 2.14 | 0.22 | 0.26 |
| HepG2_1_RNA | 190654 | 871820 | 4.57 | 38356 | 229135 | 5.97 | 0.20 | 0.26 |
| HepG2_2_RNA | 187952 | 878332 | 4.67 | 38144 | 233350 | 6.12 | 0.20 | 0.27 |
| HepG2_3_RNA | 192812 | 959790 | 4.98 | 38566 | 253313 | 6.57 | 0.20 | 0.26 |
Number of barcodes per oligo
Histogramm of number of barcodes per oligo. Median is blue, mean is red.
Activity
Violin and box plots of the log2 fold change of all oligos by the assay. Grouped by labels if set, otherwise NA. First tab shows plots using (in average) 1567 oligos with a minimum number of 5 barcodes. Second tab shows all 2016 oligos that have assigned barcodes.